Friday, January 23, 2015
How would you go about comparing proteins in a way that allows us to understand their evolution?
Proteins show similarity and differences with one another at various levels of structure and function. With this in mind, how would you go about comparing proteins in a way that allows us to understand their evolution?
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The first thing that comes to mind is to compare primary structure for any changes in the sequence and investigate if that particular mutation affects other levels of structure. As mentioned in the last post, mutation drives evolution so it'd be a good starting point.
ReplyDeleteI would also approach it from a functionality standpoint. I would start with proteins of similar functions (ie. proteases, as mentioned in class) and start backward with their quaternary structure. For example one could compare active sites of enzymes, and even their subunits to see how each structure differs to suit its particular function.
My first thought would be to identify the mutant protein, if not already known. Once I knew what I was working with, I could find out about the normal protein’s functionality and compare how the mutant affects that functionality. Once I had an idea of how the functionality was altered, I could focus on specific parts of the protein structure.
ReplyDeleteLike Susan said, starting at primary structure of a similar set of proteins would be preferable. Start with a set of proteins that have very similar overall functions but detailed, clear differences that make them unique. The more related members you start with, perhaps the easier It would be to look at the protein and genetic structures to determine where they diverged. You could combine this process with asking what these differences provide the organism in terms of fitness.
ReplyDeleteA strong understanding of basic bioinformatics tools would be very useful here as long as the proteins have been studied pretty thoroughly in terms of their structure and amino acid/nucleotide sequences. Obviously this, as stated by most people above, is pretty much looking at primary structure though similarity in secondary structures can help determined relatedness as well.
ReplyDeleteI would agree that primary structure most likely provides the greatest amount of information in regards to evolutionary changes in a protein or family of proteins over time. By observing the conservation of specific sequences or domains and relating them to specific roles, one can understand a lot about the variance in protein function over time.
ReplyDeleteI may be stating the obvious, but in order to compare groups of proteins, it might helpful to really know a single protein fairly well. Like Josh said, by using bioinformatics as a tool, we can fully study and analyze the structure of a protein and compare it to others that are similar. But you can not start comparing any proteins until you have selected one of interest. Then you can start looking at the difference and similarities in structure and how it relates to a common function between the proteins. That is, if one exists.
ReplyDeleteI feel that studying the primary structure of a well-characterized family of proteins would be the most beneficial method. For example, you could look at the primary structure of a subclass of proteases in an attempt to determine where the proteins might have possibly diverged over time. From there, a rough timeline could be established and the evolutionary reasons as to why could be speculated.
ReplyDeleteTo help understand evolution of proteins, we can look at some of the conserved regions as a starting point. Conserved regions can give us clues as to which proteins have evolved from a common lineage, and by then analyzing the differences (caused by mutations) we can better understand how and why proteins evolve.
ReplyDeleteI personally would use some of the bioinformatics tools available to compare protein structure and amino acid sequence. A multiple sequence alignment could be used to compare the amino acid sequences to look at the evolutionary relationship in which these proteins may share lineage. A phylogenetic tree can also be constructed to possible find a common ancestor or to see how closely these proteins are related. Analyzing the multiple sequence alignment can illustrate places in which mutations may have occurred such as point mutations, etc. Multiple sequence alignment can also be used to look at conserved domains within a protein structure.
ReplyDeleteI would start by looking at a protein such as arginine or leusine .Observe their organizations and the arrangement of the amino acids sequences.If there is any similar gene that performs the same function,this will confirm that they have a common ancestral and this could be my start point
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